fastq-stats1
Ea-utils: produce lots of easily digested statistics
Usage
fastq-stats [options]
<fastq-file>
Overview
Version: 1.01 $Id: fastq-stats.cpp 652 2013-09-17 17:40:32Z earonesty $
Produces lots of easily digested statistics for the files listed
Options
-c cyclemax: max cycles for which following quality stats are produced [35] -w INT window: max window size for generating duplicate read statistics [2000000] -d debug: prints out debug statements -D don't do duplicate read statistics -s INT number of top duplicate reads to display -x FIL output fastx statistics (requires an output filename) -b FIL output base breakdown by per phred quality at every cycle.
-
It sets cylemax to longest read length
-L FIL Output length counts
The following data are printed to stdout:
reads
|
: #reads in the fastq file |
|---|---|
len
|
: read length. mean and stdev are provided for variable read lengths |
phred
|
: phred scale used |
window-size
|
: Number of reads used to generate duplicate read statistics |
cycle-max
|
: Number of bases to assess for duplicity |
dups
|
: Number of reads that are duplicates |
%dup
|
: Pct reads that are duplcate |
unique-dup seq
|
: Number sequences that are duplicated |
min dup count
|
: Smallest duplicate tally for any duplicate sequence |
dup seq <rank> <count> <sequence>
|
: Lists top 10 most frequent duplicate reads along with count mean and stdev |
qual
|
: Base Quality min, max and mean |
%A,%T,%C,%G
|
: base percentages |
total bases
|
: total number of bases |
Releases
Unchanged in 5 releases since Debian 9 (Stretch).